Following the Deepwater Horizon oil spill in the Gulf of Mexico in April 2010, the USDA Natural Resources Conservation Service (NRCS) established and funded the Migratory Bird Habitat Initiative (MBHI), with the goal of improving and increasing wetland habitats on private lands to benefit wintering and migrating waterbirds displaced from oil-impacted coastal wetlands. The NRCS and conservation partners provided financial and technical assistance to landowners and managers of sites enrolled in various conservation easement programs, and incorporated approximately 190,000 ha of wetlands and agricultural lands in the Mississippi Alluvial Valley (MAV) and Gulf Coast regions in the MBHI. In fall 2010, the NRCS worked with scientists and graduate students from three universities and various conservation agencies to design and implement landscape-scale evaluations of (1) the use of MBHI-managed wetlands and comparable non-MBHI wetlands by Charadriiformes(shorebirds), Anseriformes (waterfowl), and other waterbirds; and (2) the relative effectiveness of different MBHI practices for providing habitat and food resources for migrating, resident, and wintering waterbirds. In this paper, we describe the scientific framework designed to evaluate the MBHI in improving waterbird habitats on private lands in the MAV, the Gulf Coast Prairies in Louisiana and Texas, and Gulf coastal wetlands of Mississippi and Alabama. The results of our evaluation will enhance our understanding of the influence of MBHI, other Farm Bill Conservation Initiative managed lands (e.g., Wetland Reserve Program), and selected agricultural working lands (e.g., Oryza sativa L. [Rice] fields in southern Louisiana and Texas) on wintering and migrating waterbirds. A proactive approach that uses science to evaluate governmental conservation programs is relevant and can inform development of meaningful public policy that likely will be needed for effective delivery of future conservation programs and to justify financial incentives paid to landowners to apply best management practices.